Gene Reports最新文献

{"title":"Elucidating the genetic mechanism of anti-cancer efficacy of prednisolone in acute lymphoblastic leukemia through anti-miRNA treatments","authors":"Neslihan Pinar Ozates ,&nbsp;Bakiye Goker Bagca ,&nbsp;Duygu Arican ,&nbsp;Burak Ascioglu ,&nbsp;Burak Durmaz","doi":"10.1016/j.genrep.2025.102221","DOIUrl":"10.1016/j.genrep.2025.102221","url":null,"abstract":"<div><h3>Background/aim</h3><div>Acute lymphoblastic leukemia (ALL) is a form of hematological cancer that primarily affects children. Although agents such as prednisolone are used in the treatment of this disease, chemotherapy resistance remains a concern. This study aims to elucidate the genetic mechanism underlying the previously demonstrated anticancer efficacy of anti-miRNA therapies in ALL.</div></div><div><h3>Materials and methods</h3><div>Using IPA software, we identified genes targeted by miRNAs with demonstrated anticancer activity. For modeling ALL, SUP-B15 cells were employed, whereas NCI-BL2171 cells were used to represent healthy B lymphocytes. Commercial miRNA inhibitors and Lipofectamine were used to perform the transfection. RT-qPCR was used to assess target gene expression, and fold changes were calculated using the 2^-ΔΔCt method.</div></div><div><h3>Results</h3><div>In the SUP-B15 cell line, <em>MYO10</em> gene expression was downregulated, whereas TAB2 gene expression was upregulated following the silencing of the ALL-related miRNAs in both ALL and healthy cell models<strong>.</strong> In the healthy NCI-BL2171 cell line, <em>MYO10</em> gene expression was increased.</div></div><div><h3>Conclusion</h3><div>Genomic instability resulting from <em>MYO10</em> dysregulation promotes tumor growth and contributes to immune checkpoint blockade. <em>TAB2</em> plays a role in regulating the hematopoietic system, either directly or indirectly. Understanding the functions of these genes may provide valuable insights into the mechanisms underlying cancer and hematopoiesis, potentially leading to the development of new therapies for these conditions. The mechanisms of miRNA dysregulation in ALL remain to be elucidated, and anti-miRNA-based treatments need to be developed.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102221"},"PeriodicalIF":1.0,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143817021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effects of nanoparticle based drugs on Helicobacter pylori infection and gastric cancer","authors":"Zahra Ebrahimi ,&nbsp;Hana Hamid ,&nbsp;Parisa Salari ,&nbsp;Meysam Beyrami ,&nbsp;Maryam Moradi Binabaj","doi":"10.1016/j.genrep.2025.102223","DOIUrl":"10.1016/j.genrep.2025.102223","url":null,"abstract":"<div><div>Gastrointestinal diseases affect a significant portion of the global population and pose major challenges in the medical field. Drug resistance, adverse effects, and low drug's efficacy are among the critical issues in treating these diseases. <em>Helicobacter pylori</em> (<em>H. pylori</em>) a major pathogenic bacterium, contributes to gastrointestinal diseases. Developing nano agents represents a modern perspective in therapeutic strategies, with a noteworthy role. In improving pharmacokinetics and reducing complications associated with conventional treatments. This review investigates the effects of four widely used NPs (zinc oxide (ZnONPs), gold (AuNPs), chitosan (CSNPs), and silver (AgNPs)) against <em>H. pylori</em> infection and explores their applications NP in pharmaceutical system design and optimization. These NPs exhibit a wide range of antimicrobial mechanisms, from disrupting bacterial cell integrity to generating reactive oxygen species (ROS). They also show promise in gastric cancer treatment, particularly when combined with other antibacterial agents, enhancing their anti-<em>H. pylori</em> and anticancer activities. Recently, NPs have been applied as drug carriers in drug delivery systems. This innovative use of NPs shows potential for optimizing drug efficacy and targeted cell delivery, particularly in cancer treatment.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102223"},"PeriodicalIF":1.0,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143828263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical actionability of Comprehensive Genomic Profiling in India","authors":"Prasanth S. Ariyannur ,&nbsp;Reenu Anne Joy ,&nbsp;Rahul Ramachandran,&nbsp;Thelakkattusserry Kamalasanan Sukrishna,&nbsp;Ajit Nambiar ,&nbsp;Rajasekhar Kommu,&nbsp;Moni Abraham Kuriakose,&nbsp;Venkataramanan Ramachandran,&nbsp;Prashant Kumar","doi":"10.1016/j.genrep.2025.102222","DOIUrl":"10.1016/j.genrep.2025.102222","url":null,"abstract":"<div><div>The validation and clinical utility of Comprehensive Genomic Profiling (CGP) for identifying somatic genomic mutations have been challenging within the Indian Oncology practice. The primary obstacles to establishing clinical utility are cost, availability, lack of expertise in testing, adoptability and implementation of therapeutic recommendations. However, the absence of standardized laboratory methods in Indian cases has not been previously addressed. We validated a widely applied CGP assay, TruSight Oncology 500, in a reference laboratory. Subsequently, the clinical utility in a series of 192 cases comprising late-stage tumor specimens from common solid cancer types was examined. The identified somatic variants were classified based on the AMP Tier classification to determine their clinical utility. Lung adenocarcinoma was the most common, followed by breast and gastrointestinal cancers. The most common genes with mutations were <em>TP53</em> (36.5 %), <em>MYC</em> (29.7 %), <em>EGFR</em> (20.8 %), <em>KRAS</em> (16 %), <em>PIK3CA</em> (20.6 %), <em>BRAF</em> (11 %), and <em>ERBB2</em> (10 %). Therapeutic recommendations based on AMP Guidelines Tier 1A were found in 33 % of cases, Tier 1B in 49 %, and Tier IIC in 83 % of cases. TMB-high (&gt;10muts/Mb) in 21.5 % of cases, TMB-Low (≤9 muts/Mb) in 77.6 % of cases, MSI-L (1–30 %) was identified in 85.4 % of cases, and MSS (&lt;1 %) in 14 % of cases. Overall, we identified therapeutically actionable mutations in 83 % of cases of solid tumors that had undergone CGP.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102222"},"PeriodicalIF":1.0,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143854436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a novel antimicrobial resistance associated plasmid in Pseudomonas sp. from disease tilapia (Oreochromis niloticus)","authors":"Jocelyne García Armenta ,&nbsp;Carmen E. Vargas-Peralta ,&nbsp;Roberto Cruz-Flores ,&nbsp;Olivia Cabanillas-Bernal ,&nbsp;Jesús Antonio López-Carvallo ,&nbsp;Jorge Cáceres-Martínez","doi":"10.1016/j.genrep.2025.102220","DOIUrl":"10.1016/j.genrep.2025.102220","url":null,"abstract":"<div><div>This study identifies and characterizes a novel antimicrobial resistance-associated megaplasmid in <em>Pseudomonas</em> sp. isolated from diseased Nile tilapia (<em>Oreochromis niloticus</em>) in Mexico. Aquaculture's growth has heightened concerns over antimicrobial resistance (AMR) due to the widespread prophylactic use of antibiotics to manage bacterial infections, which contributes to AMR in pathogens like <em>Pseudomonas</em> spp., an opportunistic agent of fish disease. A bacterial isolate from symptomatic tilapia was identified as closely related to <em>Pseudomonas soli</em> through 16S rRNA and 23S rRNA gene sequencing. Whole-genome sequencing revealed a 362,580 bp megaplasmid encoding 984 genes, including multidrug resistance elements, confirmed by PCR targeting key genes (<em>repA</em>, <em>parA</em> and <em>virB4</em>/<em>traC</em>). The megaplasmid exhibited high average nucleotide identity (96 %) to known resistance plasmids, underscoring the potential for horizontal gene transfer in aquaculture environments. This first identification of such a megaplasmid in tilapia pathogens highlights the urgent need for sustainable antibiotic practices in aquaculture to mitigate AMR's spread. Our findings contribute to understanding the genomic basis of AMR in <em>Pseudomonas</em> sp. and offer insights for developing management strategies to safeguard fish health and food security.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102220"},"PeriodicalIF":1.0,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143821195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of microsatellite markers by de novo transcriptome sequencing of flatfish Cyclopsetta fimbriata and Syacium papillosum (family: Paralichthyidae)","authors":"Rubí Fabiola Alderete-Domínguez ,&nbsp;Jesús Alejandro Zamora-Briseño ,&nbsp;Monica Améndola-Pimenta ,&nbsp;Juan Pablo Ek-Huchim ,&nbsp;Jaime Zaldivar-Rae ,&nbsp;Rossanna Rodríguez-Canul","doi":"10.1016/j.genrep.2025.102219","DOIUrl":"10.1016/j.genrep.2025.102219","url":null,"abstract":"<div><div>Flounder fish <em>Cyclopsetta fimbriata</em> and <em>Syacium papillosum</em> (Family: Paralichidae) inhabit the Gulf of Mexico (GoM) where there is a constant menace of oil spill events. Both can be sentinel species for pollutants associated with human activities, but the absence of markers has hampered their genetic studies. In this study we constructed two de novo transcriptomes of <em>C. fimbriata</em> and <em>S. papillosum</em> collected at 40–100 m below the sea surface and were used to develop microsatellite markers. A total of 42,273,686 and 38,304,544 raw reads were obtained for <em>C. fimbriata</em> and <em>S. papillosum</em>. After cleaning, we recovered 25,087,948 (59.3 %) reads with Q value &gt;30 for <em>S. papillosum</em> and 22,062,086 (50 %) reads with Q value &gt;30 for <em>C. fimbriata</em>. The transcriptome of <em>C. fimbriata</em> had 69,333 transcripts with an average GC content of 47.68 %. The length of contigs ranged from 248 bp to 15,452 bp, with an N50 length of 1608 bp. The <em>S. papillosum</em> transcriptome had 75,623 transcripts with an average GC content of 48.27 % with a length of contigs ranging from 181 bp to 16,638 bp, with an N50 length of 1582 bp. Then, 38 microsatellite loci for <em>C. fimbriata</em> and 40 microsatellite loci for <em>S. papillosum</em> were tested on 30 individuals of each species and 20 polymorphic microsatellite loci (50 %) were obtained for <em>S. papillosum</em> and 13 (34.21 %) for <em>C. fimbriata</em>. The Polymorphism Information Content (PIC) values were 0.8 for <em>C. fimbriata</em> and 0.9 for <em>S. papillosum</em>. Their utility for subsequent genetic population studies is discussed.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102219"},"PeriodicalIF":1.0,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143821196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole exome sequencing in 33 patients revealed 4 novel variants in 11 limbs-girdle muscular dystrophy families","authors":"Sonehra ,&nbsp;Ishtiaq Ahmed ,&nbsp;Fahimullah ,&nbsp;Abdur Rehman ,&nbsp;Ranjha Khan ,&nbsp;Ahmed Waqas ,&nbsp;Hammad Tufail Chaudhary ,&nbsp;Obaid Ur Rahman ,&nbsp;Muhammad Abbas ,&nbsp;Nabil Tariq ,&nbsp;Muhammad Tariq ,&nbsp;Muhammad Asim ,&nbsp;Gul Ghani ,&nbsp;Muhammad Sohaib ,&nbsp;Mansoor Khan ,&nbsp;Bakht Tarin Khan ,&nbsp;Taimoor Khan ,&nbsp;Gauhar Rehman ,&nbsp;Muhammad Umair ,&nbsp;Musharraf Jelani ,&nbsp;Qaiser Zaman","doi":"10.1016/j.genrep.2025.102218","DOIUrl":"10.1016/j.genrep.2025.102218","url":null,"abstract":"<div><h3>Introduction</h3><div>Muscular dystrophies (MD) are a large heterogeneous group of over 60 neuromuscular disorders caused by mutations in nearly 60 different genes. These conditions lead to varying degrees of neuromuscular dysfunctions, leading to muscular dystrophies-atrophies, gait abnormalities or waddling, tip-toe walking, difficulties in climbing stairs, dilated cardiomyopathy, and respiratory distresses.</div></div><div><h3>Methods</h3><div>In this study, we for the first time examined 67 individuals from 11 families, of whom 33 were affected ranging from 4 to 30 years. Whole exome sequencing was conducted on an index patient from each family, and the causative variants were identified using our in-house data analysis pipeline. The candidate variants were further validated through Sanger sequencing in the family to confirm the segregation of the affected alleles.</div></div><div><h3>Results</h3><div>Patients primarily showed progressive weakening of muscles, changes in muscle tone or structure and the development of an abnormal gait, eventually leading to loss of ambulation. The severity of the disease varied both within and between families. This study identified four novel pathogenic variants (<em>COL6A1</em>; c.1659_1665dup; p.Pro555_Asp557dup, <em>DMD</em>; 145.7Kb cytogenetic band Xp21.1 deletion, <em>DMD:</em> 40.3Kb cytogenetic band Xp21.1 duplication and <em>HMGCR</em>; c.1537C &gt; T; p.Pro513Ser) and six recurrent variants (<em>DMD</em>; c.1032 T &gt; A; p.Tyr344Ter, <em>DMD</em>; c.3923C &gt; A; p.Ser1308Ter, <em>CAPN3</em>; c.379 + 3 A &gt; G, <em>DYSF</em>; c.4251del; p.Ile1418SerfsTer47, <em>ANO5</em>; c.692G &gt; T; p.Gly231Val. and <em>LAMA2</em>; c.1300C &gt; T; p.Arg434Ter) in seven MDs associated genes (<em>COL6A1</em>, <em>DMD</em>, <em>CAPN3</em>, <em>DYSF</em>, <em>HMGCR</em>, <em>ANO5</em>, and <em>LAMA2</em>).</div></div><div><h3>Discussion</h3><div>In this study, we identified four novel and six recurrent pathogenic variants in seven genes, expanding the genetic basis of MD and providing a valuable resource for further diagnostic and therapeutic approaches. These findings have significant implications for enhancing the understanding of MD pathogenesis and may guide the development of personalized therapeutic strategies for affected individuals. Overall, this study contributes to advancing the genetic diagnostics of MD and offers new avenues for therapeutic interventions, potentially improving patient outcomes.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102218"},"PeriodicalIF":1.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143792330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of microRNA-196a-2 rs11614913 and microRNA-499a rs3746444 polymorphisms in an Egyptian population with Behçet's Disease: A single-center case-control study","authors":"Dina M.T. Koptan ,&nbsp;Noha M. Shaheen ,&nbsp;Reem J Farid ,&nbsp;Nancy Mostafa Abouzaid ,&nbsp;Riham S.H.M. Allam ,&nbsp;Fatema T Elgengehy ,&nbsp;Basma M Medhat ,&nbsp;Noha M Abdel Baki","doi":"10.1016/j.genrep.2025.102217","DOIUrl":"10.1016/j.genrep.2025.102217","url":null,"abstract":"<div><h3>Aim</h3><div>Single nucleotide polymorphisms can significantly influence the processing, expression, and maturation of microRNAs (miRNAs) and may also contribute to the pathogenesis of various diseases including Behçet's disease (BD). The present study aimed to investigate the association of <em>mir-196a-2</em> rs11614913 (C/T) and <em>mir-499a</em> rs3746444 (A/G) polymorphisms with BD susceptibility, demographic characteristics, and clinical manifestations in a cohort of Egyptian patients.</div></div><div><h3>Methods</h3><div>We genotyped the polymorphisms in 68 Egyptian patients with BD and 128 healthy controls using TaqMan real-time polymerase chain reaction.</div></div><div><h3>Results</h3><div>Carriage of the combined <em>mir-196a-2</em> rs11614913 TT and <em>mir-499a</em> rs3746444 AA genotypes conferred a 3-fold increased risk for BD development (p = 0.009). Carriers of the <em>mir-196a-2</em> CT genotype developed BD at an older age compared to CC carriers (p = 0.03). The CC + CT genotypes of <em>mir-196a-2</em> were more prevalent among patients with ocular involvement (p = 0.02), while the CT genotype was associated with an increased risk of neuro-BD (p = 0.02, OR = 3.3).</div></div><div><h3>Conclusion</h3><div>Our results suggest that the combined <em>mir-196a-2</em> rs11614913 TT and <em>mir-499a</em> rs3746444 AA genotypes may be associated with an increased risk of BD, while <em>mir-196a-2</em> rs11614913 genotypes may be linked to the age of BD onset and specific clinical manifestations. Further studies with larger cohorts are needed to confirm our findings.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102217"},"PeriodicalIF":1.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143850397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinicopathological effects of FOXO4 downregulation and FOXO6 upregulation in Indian breast cancer patients","authors":"Sheersh Massey ,&nbsp;Maria Habib ,&nbsp;Samiha Saad ,&nbsp;Arzoo Bano ,&nbsp;Mohammad Aasif Khan ,&nbsp;Syeda Maryam Husain ,&nbsp;Sadaf ,&nbsp;Kapil Dev ,&nbsp;N.K. Shukla ,&nbsp;Syed Akhtar Husain","doi":"10.1016/j.genrep.2025.102212","DOIUrl":"10.1016/j.genrep.2025.102212","url":null,"abstract":"<div><div>FOXO (Forkhead box O) proteins modulates wide range of cellular functions including metabolism, longevity, growth and proliferation. Their aberrant expression, mutations or deletions are frequently reported in various human cancers making them crucial therapeutic candidates. In this study we aim to determine the expression pattern of comparatively less explored FOXO family proteins, FOXO4 and FOXO6 and their clinicopathological significance in Indian breast cancer patients. Breast tumor tissue and adjacent normal tissue samples were collected from the collaborating institute. FOXO4 and FOXO6 mRNA and protein expression were determined using Real Time PCR and Immunohistochemistry respectively. Further, GEPIA2 (Gene Expression Profiling Interactive Analysis 2) was used to corroborate the experimental results and prognostic significance of FOXO4 and FOXO6 was determined using KM-plotter. The mRNA expression of FOXO4 was found to be 3.25 fold downregulated while that of FOXO6 was 2.7 fold upregulated in breast cancer samples. The Immunohistochemistry results revealed weak expression of FOXO4 protein in 37 out of 52 cases and strong staining was observed for FOXO6 protein in 29 out of 52 cases. Lymph node status of the patients exhibited significant association with FOXO4 mRNA (<em>p</em> = 0.011) and protein level (<em>p</em> = 0.006). Whereas in case of FOXO6, enhanced expression showed substantial relation with ER status at protein level (<em>p</em> = 0.037) and with menopausal status of the patients at both mRNA (<em>p</em> = 0.042) and protein level (<em>p</em> = 0.015). Similar expression trend was observed in GEPIA2 database for both the genes. KM-plotter analysis further revealed that FOXO4 is significantly linked to relapse free survival of the patients. FOXO4 and FOXO6 genes manifest contrasting expression patterns, with lowered FOXO4 and elevated FOXO6 expression in Indian breast cancer samples. This study aims to provide insights into the clinical relevance of expression of both the genes. Future studies investigating their molecular interactions could be helpful in determining their relative significance as putative biomarkers in diagnosis and treatment of breast cancer.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102212"},"PeriodicalIF":1.0,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143792331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling the interplay of antimicrobial resistance and stress response in the saline desert metagenomes of Gujarat, India","authors":"R. Sahana ,&nbsp;Vishal Mevada ,&nbsp;Urvisha Beladiya ,&nbsp;Dhaval Prajapati ,&nbsp;Himani Gandhi ,&nbsp;Rajesh Patel","doi":"10.1016/j.genrep.2025.102216","DOIUrl":"10.1016/j.genrep.2025.102216","url":null,"abstract":"<div><div>The metagenomic analysis of the present study states the intricate community of salt-tolerant bugs living in saline soils from Kutch, Gujarat. Metagenomics sequencing has already been explored in this region for community analysis. However, we analyzed the metagenome of a saline desert and compared it with publicly available published metagenomes to identify common antimicrobial resistance found in the saline desert. The bioinformatics-based analysis revealed the presence of various antibiotic resistance (AMR) genes in <em>Escherichia coli</em> EF-Tu mutants, which confer resistance to several compounds, including Pulvomycin, FosG, rsmA, qacJ, and qacG. Additionally, the vanW gene in the vanI cluster and the vanY gene in the vanM cluster were identified. These mutants exhibit different resistance mechanisms, such as antibiotic inactivation (VanA — VIM-VIA), alteration of antibiotic targets (cfr and VanB), and the involvement of antibiotic efflux pumps, etc. The prevalence of AMR genes related to efflux pump indicates the importance of this genes (copR, bcrA, cesC, merA, narA, tetA, trxLHR and yfeB) toward salt tolerance and antibiotic resistance. This effect was robust even when human impacts were not substantial, illustrating the overwhelming adaptability of these organisms. The variable presence of these genes throughout the samples highlights an environmental effect on their distribution, suggesting a resistance mechanism. This work paves the way to understanding antimicrobial resistance genes produced in these pristine, human-untouched places.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102216"},"PeriodicalIF":1.0,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143767804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative real-time PCR analysis of circulating MicroRNA levels in blood samples from pediatric patients with epilepsy","authors":"Haidar J. Muhammed ,&nbsp;Marwa M. Al-Attar ,&nbsp;Zainab Fayadh Shubrem ,&nbsp;Mohanad Kareem Aneed Al-Saedi ,&nbsp;Maryam Qasim Mohammed","doi":"10.1016/j.genrep.2025.102214","DOIUrl":"10.1016/j.genrep.2025.102214","url":null,"abstract":"<div><h3>Background</h3><div>Epilepsy in childhood is common in the first year and its incidence decreases with age increase. The prevalence of epilepsy in Iraq was 1.0 per 1000 children according to a previous investigation. MicroRNAs play crucial roles in various biological processes, including brain development and function, and have emerged as potential key players in the complex pathophysiology of epilepsy. This study aimed to investigate the expression levels of miRNAs in their mature forms including <em>miR-30a-5p</em> and <em>miR-577</em>, in epilepsy patients and to explore their potential as biomarkers for the disease.</div></div><div><h3>Methods</h3><div>Eighty participants were enrolled in the study classified as (<em>n</em> = 40) Epilepsy patients along with (n = 40) as healthy controls (HCs). The miRNA was extracted from whole blood, converted to complementary DNA (cDNA) using a specialized kit, and quantified using quantitative real-time PCR (qRT-PCR) for <em>miR-30a-5p, miR-577,</em> and the reference gene <em>snRNA-U6</em>.</div></div><div><h3>Results</h3><div>The results revealed a significant upregulation of <em>miR-30a-5p</em> in epilepsy patients compared to healthy controls with (<em>p</em>-value, 0.01). The <em>miR-577</em> expression did not differ between groups (<em>p</em>-value, 0.2). A weak negative correlation between the two miRNAs was observed, suggesting a potential inverse correlation. Receiver Operating Characteristic (ROC) curve analysis indicated that <em>miR-30a-5p</em> may serve as a biomarker for epilepsy.</div></div><div><h3>Conclusion</h3><div>This study suggests that <em>miR-30a-5p</em>, showing upregulation and according to the ROC curve may act as an early epilepsy detection biomarker. Conversely, miR-577, despite a decrease in expression, is deemed unsuitable as a biomarker due to its lack of statistical significance and poor diagnostic performance.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102214"},"PeriodicalIF":1.0,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143767803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}